05.01.14 9:45 AM ET

Concerns are growing among Western intelligence services that Syria still has a significant and undeclared arsenal of chemical weapons, including crude chlorine-filled bombs, secret stockpiles of sophisticated nerve gasses or their components—and the scientific know-how to rebuild a larger-scale, higher-grade chemical weapons effort once the Bashar al-Assad regime has escaped the international spotlight.

“A ghost of CW [chemical weapons] program in a place riven with conflict—that’s a real concern,” one American intelligence official tells The Daily Beast.

But it’s not the only worry. Within the U.S. intelligence community, there’s also lingering unease about the Assad regime’s biological weapons program that has never been the focus of international inspections and that American officials confess they just don’t have the resources to track down.

To be sure, the deadly and publicly-declared chemical arsenal that Assad had a year ago, that allegedly was used to kill hundreds of people in August, and that he agreed to destroy in September under threat of an American attack is “no longer in existence,” according to the inspectors on the ground in Damascus. Only 7.5 percent of the 1,300 metric tons of chemical agents and precursors that the regime declared remain in the country, and the means of combining those elements to make sophisticated weapons of mass destruction like vx and sarin gas has been destroyed.

But the inspectors are only commenting on the chemical arsenal Assad admitted he had. There’s mounting concern that the Syrian regime may have a second unconventional weapons program—one Assad never told the international community about. Just before the Syrians missed a deadline they had set last Sunday to hand over all declared chemicals, Dutch diplomat Sigrid Kaag, head of the Organization for the Prohibition of Chemical Weapons-United Nations mission to Syria, told reporters that “if you put some of the [remaining] chemicals together you can still produce very dangerous chemical weapons agents.” However, “in order to produce, to prepare, to launch you need the production facilities, you need the munition and filling capabilities, you need the tactical munitions—all those have been destroyed. So what remains at one site are elements of a chemical weapon, put the chemical weapons program of Syria as per the current declaration of Syria to the OPCW under the Chemical Weapons Convention, is no longer in existence” [our italics].

Asked for clarification of this statement, another official at the OPCW told The Daily Beast that Syria “destroyed all of its production facilities, mixing and filling equipment, and munitions designed for use with CW agents before Christmas” and has moved all but 92.5 percent of the weapons and constituent chemicals of its program out of the country. Mostly they have been put on Danish and Norwegian ships from which they will be transferred to a specially equipped American vessel, the Cape Ray, for final destruction before the June 30 deadline set by the U.N. Security Council.

“But the U.S. France and UK contend they have intelligence that indicates Syria did not declare all of its CW materiel to the OPCW and continues to hide assets,” said the same official in an e-mail. “Those allegations remain to be examined and there are intensive discussions on options for doing that.” Because of these suspicions, the remaining 7.5 percent has become “like the fat lady at the opera, it ain’t over until Syria has completely fulfilled its obligations to disarm.”

“We know about the programs, we know about the people, and we know about the munitions,” an American intelligence official told The Daily Beast. “But the production quantity of materials? That’s the area where we’re the haziest. … Accountancy is a big issue. We have conflicting information and we don’t know what to trust.”

Such allegations inevitably evoke comparisons with the bogus intelligence used to justify the American-led invasion of Iraq in 2003. There is the critical difference that in this case the U.S. administration is not looking for a pretext to go to war. Indeed, far from it. But the issue of remaining Syrian WMD raises the question once again of whether the United States regards these weapons as a “red line” justifying armed intervention or not.

Washington’s relations with Moscow, severely strained by the Ukraine crisis, are another complicating factor. Russia played a key role in brokering the deal that was supposed to eliminate Assad’s chemical weapons capability once and for all, and helped avert an American bombing campaign last fall.

The appearance of chlorine as a weapon on the Syrian battlefield has further complicated matters; the latest alleged attack occurred Wednesday in al-Tamanah, injuring 70 people and killing one. Chlorine is a widely available industrial chemical not normally classified as a weapon of mass destruction, although it was the first poison gas used on the battlefields of World War I. In contact with water—tears in the eyes or moist tissue in the lungs —it turns to acid with devastating effect, blinding and asphyxiating its victims. But chlorine’s pungent smell and green color are easy to detect, according to the U.S. government’s Centers for Disease Control, which makes it easier to identify and to escape.

Videos have surfaced on YouTube of “barrels with fins being pushed out of military helicopters” in areas where the Assad regime is alleged to have used chlorine, according to one American official. The Syrian government insists that the gas was used instead by the rebels it deems terrorists. There is a precedent for that: In late 2006 and early 2007, Iraqi insurgents who are now closely allied with the most radical elements in the Syrian uprising added chlorine to their car bombs and truck bombs on several occasions.

But of course, the rebels in Syria have no air force, and the alleged chlorine attacks were delivered from the air.

Concerns about Syria’s actual compliance with the chemical weapons treaty are heightened by the example of Libya, which supposedly had destroyed its chemical arsenal under dictator Muammar Qaddafi. In 2012, however, after he was brought down by a popular uprising and NATO airpower, international inspectors found “several hundred munitions loaded with [the chemical agent] sulfur mustard [and] few hundreds kilograms of sulfur mustard stored in plastic containers,” according to the OPCW.

Since then, the U.S. official said, “we’ve set a higher bar” before concluding a chemical arsenal has been eliminated.

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The official noted that extremely deadly nerve agents like VX and sarin, which was used last August, “start from the same building block, so the accountancy issue for one is the same as for the other.” Both are colorless and odorless and similar to pesticides, but designed to kill humans rather than insects—or, one might say, as if they were insects.

The horrifying reality of what chemical and biological weapons can do to people contrasts with the tangled treaty issues and technicalities that govern efforts to control them, as the Syrian example demonstrates all too clearly.

When United Nations inspectors went to Syria last summer and fall searching for evidence that chemical weapons had been used, there was a long list of things they were not supposed to look at. The U.N. ground rules said they couldn’t make any judgment about who actually employed chemical weapons. The chlorine arsenal—that was off-limits. And as for biological weapons—which have the potential to be the most fearsome part of Assad’s secret arsenal—there was no mandate to search for them at all.

Current and former U.S. officials all say they’re convinced Assad has some sort of biological weapons program. They just don’t have the resources to investigate it. “BW”—shorthand for biological weapons—“have completely fallen off our radar. It’s striking to me,” says a former U.S. defense official who worked the Syria file. “We were talking about it a bit. Now it’s gone away. I don’t know why.”

And don’t count on the U.S. or its allies doing much about Syria’s BW efforts any time soon. The ongoing removal and destruction of Assad’s chemical weapons has monopolized all of the WMD-hunters’ attention. “Obviously we’re not going to push very hard right now, because we’ve got to get removal done first,” one U.S. intelligence official tells The Daily Beast. “The IC [intelligence community] put a lot of resources towards removal. Counter-proliferation [of BW] becomes a second-tier priority.”

A spokesman for the U.N.’s Biological Weapons Convention implementation support unit based in Geneva says his organization hasn’t been particularly focused on Syria, either. “Nobody has raised anything specific about biologic weapons in Syria, certainly not in any official context here,” he added.

The United States has put Syria on its lists of countries believed to possess biological weapons in the past and “naturally, given the experience with chemical weapons, people are concerned,” said the official in Geneva. But biological weapons and chemical weapons are covered by two separate treaties, and the biological treaty, unlike the chemical one, has no component like the OPCW to monitor compliance. Even if it did, Syria has signed but not ratified the Biological Weapons Convention, so it doesn’t have to abide by any of its weak provisions.

In point of fact, nobody has alleged Assad is using biological weapons, while many people alleged he was using poison gas last year. And despite years of speculation, nobody has proved Assad has any germ warfare capability at all. But out of sight doesn’t mean out of mind in this case, at least not completely. The “what-ifs” of biological mass destruction are so gruesome that there’s concern in some security circles that the focus on eliminating Assad’s chemical weapons has overshadowed and obscured the danger of the biological program he’s assumed to have.

The al Qaeda conglomerate has been trying to develop biological weapons since before 9/11. A lab was operating in Afghanistan in those days. It even had its master bug-maker, the Malaysian Yazid Sufaat, who has been in and out of prisons in his home country. Then in 2009, dozens of AQ acolytes in Algeria were reported to have died of bubonic plague when an experiment went awry, although the organization vehemently denied those stories.

The Israelis, who have obvious reasons to keep close tabs on the weapons of mass destruction next door, have raised the alarm about the Syrian biological program many times. “The biological warfare agents that are believed to have been developed by Syria include virulent pathogens, such as anthrax germs, and the lethal biological toxins botulinum and ricin,” writes Dany Shoham at the Begin-Sadat Center for Strategic Studies. “Western estimations suggest that Syria has significant quantities of these biological warfare agents, although the evidence for this is inconclusive.” Shoham adds without substantive evidence that “Syrian possession of the smallpox virus is likely.”

According to the CDC, “smallpox was declared globally eradicated in 1980; however there are concerns that smallpox virus could be used for bioterrorism.” (The only places the smallpox virus are known to exist today are storage facilities at the CDC and in Russia.)

U.S. Director of National Intelligence James Clapper said at the end of January this year: “We judge that some elements of Syria’s biological warfare (BW) program might have advanced beyond the research and development stage and might be capable of limited agent production, based on the duration of its longstanding program.” But “to the best of our knowledge, Syria has not successfully weaponized biological agents in an effective delivery system” even thought “it possesses conventional weapon systems that could be modified for biological-agent delivery.”

At least one U.S. intelligence official says that Clapper might have gotten just a bit ahead of his skis. While Assad made some progress on weaponizing ricin—a toxin derived from the castor bean—his scientists “never got past R&D phase for anything else.” About five years ago, the official says, Syria made the switch from developing “botanicals” like ricin to “microbial” weapons like anthrax. “They still haven’t settled on anything—they’re researching agents, and whether they can mass-produce them. It’s the very early kernel of a BW program.” In part, the official said, that’s because the U.S. and its allies have been able to prevent Syria from acquiring the equipment needed for mass production, like large fermenters. “I think we’ve blocked anything above what goes on a lab bench,” the official added.

At the great moment of crisis over Assad’s chemical weapons program after the mass killing at Ghouta last August—as the U.N. inspectors were determining that, yes, chemical weapons had been used, and all signs pointed to the Assad regime as the culprit—Washington might have tried to insist that Assad come clean on his biological program as well as his chemical one. But it did not. The French tried to pick up the ball. They wanted the crucial U.N. Security Council resolution that called on Assad to eliminate his chemical arsenal to focus on his biological program as well. But the Russians would not hear of such a thing, whether for nefarious motives or practical motives or both.

The biological threat in Syria has been hard to sell to the general public, says Olivier Guitta, head of research at the Henry Jackson Society in London. He suggests that one reason it is not more publicized is because governments are afraid to let people know just how dangerous and destructive these weapons could be in the hands of terrorists. “The potential implications for the world economy, on trade, and on travel,” he said, “are such that governments are trying to keep the issue under wraps and address it quietly.”

But some of the biggest concerns in the American intelligence community aren’t about what individual chemicals or germs that the Assad regime might have squirreled away. They’re about Syria’s biologists, chemists and engineers—the people who helped build up Assad’s massive unconventional weapons program, and could do so again, given the proper resources and time.

Other counter-WMD projects over the years have attempted to find new ways for these scientists and engineers to make themselves useful; after the Cold War, the U.S. spent $309 million to retask approximately 17,000 scientists from the Soviet Union. Today, there’s no similar effort going in Syria. And without it, Western intelligence analysts will be hard-pressed to put nightmares of Syrian WMD out of their heads.